Scientific Publications 2005
2005. "Application of Extended Inverse Scatter Correction to Mid-Infrared Reflectance Spectra of Soil." Journal of Chemometrics 19(5-7):271-281. doi:10.1002/cem.929 Abstract Scattering artifacts adversely affect infrared reflectance measurements of powders and soils, and extended inverse scatter correction (EISC) is a flexible method useful for correcting for these artifacts. EISC was used to correct mid-infrared reflectance spectra of two different soils coated with dibutyl phosphate and the results were examined using regression analysis. To determine the correction, EISC fits a measured spectrum to a reference spectrum. However, if measured spectra contain features not included in the reference spectrum the fit can be biased resulting in poor correction. Weighted and robust least squares were used to account for these potential biases. Additionally, the present work demonstrates how analyte-free samples can be used to determine basis functions for an extended mixture model used in the correction. Corrected spectra resulted in partial least squares models that performed at least as well as 2nd derivative spectra and were more interpretable.
2005. "Annealing Simulations of Nano-Sized Amorphous Structures in SiC." Nuclear Instruments and Methods in Physics Research. Section B, Beam Interactions with Materials and Atoms 228(1-4):282-287. Abstract A two-dimensional model of a nano-sized amorphous layer embedded in a perfect crystal has been developed, and the amorphous-to-crystalline (a-c) transition in 3C-SiC at 2000 K has been studied using molecular dynamics methods, with simulation times of up to 88 ns. Analysis of the a-c interfaces reveals that the recovery of the bond defects existing at the a-c interfaces plays an important role in recrystallization. During the recrystallization process, a second ordered phase, crystalline 2H-SiC, can be nucleated and grow, and is stable for long simulation times. The crystallization mechanism is a two-step process that is separated by a longer period of second-phase stability. The kink sites formed at the interfaces between 2H- and 3C-SiC provide a low energy path for 2H-SiC atoms to transfer to 3C-SiC atoms, which can be defined as a solid-phase epitaxial transformation (SPET). It is observed that the nano-sized amorphous structure can be fully recrystallized at 2000 K in SiC, which is in agreement with experimental observations.
2005. "Atomic-Level Computer Simulation of SiC: Defect Accumulation, Mechanical Properties and Defect Recovery." Philosophical Magazine. Structure and Properties of Condensed Matter 85(4-7):509-518. Abstract Damage accumulation simulated previously has been used to study volume swelling of 3C-SiC, and to calculate the elastic constants, bulk and elastic moduli of the cascade-amorphized SiC. The swelling increases rapidly with dose at low-dose levels, but the rate of increase decreases dramatically at higher dose with a saturation volume change of 8.2% for the cascade-amorphized state. The elastic constants in the cascade-amorphized SiC decrease about 22% for C11 and C12, 43% for C44, and 23% for bulk and elastic moduli. In order to understand defect annealing of damage accumulation, the stable Frenkel pairs created at low energy events have been annealed at different temperatures, using MD methods, to determine the time required for interstitials to recombine with vacancies. The results show that the low activation energies qualitatively overlap with experimental values observed during low temperature recovery. Thus, the present results suggest that low temperature recovery processes are associated with the spontaneous recovery of Frenkel pairs.
2005. "Defect Properties in GaN: Ab Initio and Empirical Potential Calculations." Materials Science Forum 475-479(1-5):3087-3090. Abstract The defect properties and atomic configurations in GaN have been comparatively investigated using density functional theory (DFT) and molecular dynamics method with two representative potentials. The DFT calculations show that the relaxation of vacancies is generally small, but the relaxation around antisite defects is large. The N interstitials, starting from any possible configurations, eventually relax into a N+-N<11-20 > split interstitial. In the case of Ga interstitials, the most stable configuration is a Ga octahedral interstitial, but the Ga+-Ga<11-20 > split interstitial can bridge the gap between non-bounded Ga atoms. The formation energies of vacancies and antisite defects obtained using the Stillinger-Weber potential (SW) are in reasonable agreement with those obtained by DFT calculations, whereas the Tersoff-Brenner (TB) potential better describes the behavior of N interstitials.
2005. "Erosion Rate Variations during XPS Sputter Depth Profiling of Nanoporous Films." Surface and Interface Analysis 37(4):417-423. Abstract Sputter depth profiling is commonly used to obtain valuable information regarding the three dimensional distribution of elements within a sample, and is one of the best ways to measure the composition of a buried interface or the uniformity of a thin film. X-ray photoelectron spectroscopy (XPS) is one of the analysis tools often used in conjunction with ion beam erosion to obtain sputter depth profiles. However, to obtain accurate depth information it is often necessary to better understand the sputtering process for a specific materials system. Artifacts such as differential sputtering, varying sputter rates and ion beam-induced chemistry are well known. Here, however, we present evidence from experiments on a porous thin film deposited on a Si wafer that relatively small chemical and/or structural changes in a nanoporous film can affect the rate of erosion measured during sputter depth profiling. Reproducible variations in sputter rate are found with chemical modification leading to compositional changes of the nanoporous thin film. The origin of the sputter rate changes is discussed with the aid of results obtained using Fourier transform infrared spectroscopy, profilometry, nuclear reaction analysis, electron microscopy and XPS-based depth profiling.
2005. "Substrate Hydroxylation in Methane Monooxygenase:Quantitative Modeling via Mixed Quantum Mechanics/Molecular Mechanics Techniques." Journal of the American Chemical Society 127(3):1025-1037. doi:10.1021/ja049847b Abstract The research described in this product was performed in part in the Environmental Molecular Sciences Laboratory, a national scientific user facility sponsored by the Department of Energy's Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory. Using broken-symmetry unrestricted density functional theory quantum mechanical (QM) methods in concert with mixed quantum mechanics/molecular mechanics (QM/MM) methods, the hydroxylation of methane and substituted methanes by intermediate Q in methane monooxygenase hydroxylase (MMOH) has been quantitatively modeled. This protocol allows the protein environment to be included throughout the calculations and its effects (electrostatic, van der Waals, strain) upon the reaction to be accurately evaluated. With the current results, recent kinetic data for CH₃X (X ) H, CH₃, OH, CN, NO₂) substrate hydroxylation in MMOH (Ambundo, E. A.; Friesner, R. A.; Lippard, S. J. J. Am. Chem. Soc. 2002, 124, 8770-8771) can be rationalized. Results for methane, which provide a quantitative test of the protocol, including a substantial kinetic isotope effect (KIE), are in reasonable agreement with experiment. Specific features of the interaction of each of the substrates with MMO are illuminated by the QM/MM modeling, and the resulting effects upon substrate binding are quantitatively incorporated into the calculations. The results as a whole point to the success of the QM/MM methodology and enhance our understanding of MMOH catalytic chemistry. We also identify systematic errors in the evaluation of the free energy of binding of the Michaelis complexes of the substrates, which most likely arise from inadequate sampling and/or the use of harmonic approximations to evaluate the entropy of the complex. More sophisticated sampling methods will be required to achieve greater accuracy in this aspect of the calculation.
2005. "How radiation kills cells: Survival of Deinococcus radiodurans and Shewanella oneidensis under oxidative stress." FEMS Microbiology Reviews 29(2):361-375. Abstract The radiation resistant bacterium Deinococcus radiodurans accumulates very high intracellular manganese and relatively low iron levels compared to the dissimilatory metal-reducing bacterium Shewanella oneidensis which is extremely sensitive. For Fe-rich, Mn-poor cells, death at low doses might be caused by the release of Fe(II) from proteins during irradiation, followed by Fe(II)-dependent reduction of hydrogen peroxide produced by metabolism after irradiation. In contrast, Mn(II) ions concentrated in D. radiodurans might serve as antioxidants that reinforce enzymic systems which defend against oxidative stress during recovery. We extend our hypothesis here to include consideration of respiration, tricarboxylic acid cycle activity, peptide transport, and metal reduction, which together with Mn(II) transport represent potential new targets to control cell recovery from radiation injury.
2005. "A Mapping of the Electron Localization Function for Earth Materials ." Physics and Chemistry of Minerals 32(3):208-221. doi:10.1007/s00269-005-0463-x Abstract The electron localization function, ELF, generated for a number of geometry-optimized earth materials, provides a graphical representation of the spatial localization of the probability electron density distribution as embodied in domains ascribed to localized bond and lone pair electrons. The lone pair domains, displayed by the silica polymorphs quartz, coesite and cristobalite, are typically banana-shaped and oriented perpendicular to the plane of the SiOSi angle at ~0.60 Å from the O atom on the reflex side of the angle. With decreasing angle, the domains increase in magnitude, indicating an increase in the nucleophilic character of the O atom, rendering it more susceptible to potential electrophilic attack. The Laplacian isosurface maps of the experimental and theoretical electron density distribution for coesite substantiates the increase in the size of the domain with decreasing angle. Bond pair domains are displayed along each of the SiO bond vectors as discrete concave hemispherically-shaped domains at ~0.70 Å from the O atom. For more closed-shell ionic bonded interactions, the bond and lone pair domains are often coalesced, resulting in concave hemispherical toroidal-shaped domains with local maxima centered along the bond vectors. As the shared covalent character of the bonded interactions increases, the bond and lone pair domains are better developed as discrete domains. ELF isosurface maps generated for the earth materials tremolite, diopside, talc and dickite display banana-shaped lone pair domains associated with the bridging O atoms of SiOSi angles and concave hemispherical toroidal bond pair domains associated with the nonbridging ones. The lone pair domains in dickite and talc provide a basis for understanding the bonded interactions between the adjacent neutral layers. Maps were also generated for beryl, cordierite, quartz, low albite, forsterite, wadeite, åkermanite, pectolite, periclase, hurlbutite, thortveitite and vanthoffite. Strategies are reviewed for finding potential H docking sites in the silica polymorphs and related materials. As observed in an earlier study, the ELF is capable of generating bond and lone pair domains that are similar in number and arrangement to those provided by Laplacian and deformation electron density distributions. The formation of the bond and lone pair domains in the silica polymorphs and the progressive decrease in the SiO length as the value of the electron density at the bond critical point increases indicates that the SiO bonded interaction has a substantial component of covalent character.
2005. "Experimental and Theoretical Bond Critical Point Properties for Model Electron Density Distributions for Earth Materials ." Physics and Chemistry of Minerals 32(2):114-125. Abstract Generalized X-ray scattering factor model experimental electron density distributions and bond critical point, bcp, properties generated in recent studies for the earth materials stishovite, forsterite, fayalite and cuprite with high energy single crystal synchrotron X-ray diffraction data and those generated with high resolution diffraction data for coesite and senarmonite were found to be adequate and in relatively good agreement, ~5% on average, with those calculated with quantum chemical methods with relatively robust basis sets. High resolution low energy single crystal diffraction data, recorded for the molecular sieve AlPO4-15, were also found to yield model electron density distribution values at the bcp points for the AlO and PO bonded interactions that are in relatively good to moderately good agreement with the theoretical values, but the Laplacian values of the distribution at the points for the two bonded interactions were found to be in relatively poor agreement. In several cases, experimental bcp properties, generated with conventional low energy X-ray diffraction data for several rock forming minerals, were found overall to be in poorer agreement with the theoretical properties. The overall agreement between theoretical bcp properties generated with computational quantum methods and experimental properties generated with synchrotron high energy radiation not only provides a basis for using computational strategies for studying and modeling structures and their electron density distributions, but it also provides a basis for improving our understanding of the crystal chemistry and bonded interactions for earth materials. Theoretical bond critical point properties generated with computational quantum methods are believed to rival the accuracy of those determined experimentally. As such the calculations provide a powerful and efficient method for evaluating electron density distributions and the bonded interactions for a wide range of earth materials.
2005. "A REDOR NMR Study of a Phosphorylated Statherin Fragment Bound to Hydroxyapatite Crystals." Journal of the American Chemical Society 127(26):9350-9351. doi:10.1021/ja050910m Abstract Acidic proteins found in mineralized tissues act as nature’s crystal engineers, where they play a key role in promoting or inhibiting the growth of minerals such as hydroxyapatite (HAP), Ca10(PO4)6- (OH)2, the main mineral component of bone and teeth. There is remarkably little known about the protein structure-function relationships and the recognition processes governing hard tissue engineering. It is well-known that several salivary proteins (statherin) and peptides (SN-15, N-terminal 15 amino fragment of statherin) bind strongly to HAP to regulate crystal growth.1 In this work, we describe how solid-state NMR can be used to identify which amino acid side chains of SN-15 (DpSpSEE15NKFLRRIGRFG) interact with the HAP surface, even in the presence of phosphorylated side chains. Prior structural studies have indicated that the second through twelfth amino acids are R-helical in full length statherin on HAP, while the SN-15 fragment is in an extended structure toward the N-terminus, only gaining R-helical structure at the seventh amino acid. Additionally, prior dynamics studies have indicated that the region from the seventh amino acid to the C-terminus interacts less strongly with the HAP surface than the first six amino acids.
2005. "Molecular-Level Descriptions of Surface Chemistry in Kinetic ModelsUsing Density Functional Theory." Chemical Engineering Science 59(22-23):4679-4691. doi:10.1016/j.ces.2004.09.038 Abstract A portion of this work was conducted at EMSL, a national scientific user facility. Electronic structure calculations based on Density Functional Theory (DFT) are increasingly used to probe reaction mechanisms on catalyst surfaces. These calculations provide information about geometries, stabilities, and reactivities of adsorbed species on various surfaces. Conducting microkinetic analysis in conjunction with DFT calculations forms a powerful combination of methodologies to allow quantitative information to be derived about catalytic reactions at the molecular level. Specifically, whereas the microkinetic approach does not make any a priori assumptions about which steps may be rate controlling or which species may be abundant on the surface, there is usually not sufficient information to extract values of all kinetic parameters from experimental data. In contrast, results from DFT calculations alone cannot be used to assess the relative rates of various pathways, because these rates depend on reaction conditions. Instead, the results from DFT calculations form initial estimates of parameters for the microkinetic model, and the microkinetic model is used to predict rates of elementary steps and surface coverages under various reaction conditions, thereby forming a bridge with reaction kinetics data and surface spectroscopic measurements. In this paper, we outline some of the concepts useful for understanding DFT calculations and for using the results of these calculations in reaction modeling. We also introduce key concepts in microkinetic analysis, and we illustrate how microkinetic models are used to probe reaction pathways, reaction orders, and surface coverages for the decomposition of methanol on platinum.
2005. "Ion/Surface Reactions and Ion Soft-Landing." Physical Chemistry Chemical Physics. PCCP 7:1490-1500. Abstract Ion/surface collision phenomena in the hyperthermal collision energy regime (1-100 eV) are reviewed, with emphasis on chemical processes associated with the impact of small organic and biological ions at functionalized self-assembled monolayer surfaces. Inelastic collisions can lead to excitation the projectile ion and can result in fragmentation, a process known as surface-induced dissociation which is useful in chemical analysis using tandem mass spectrometry.. Changes in charge can accompany ion/surface collisions and those associated with a change in polarity (positive to negative ions or vice-versa) are an attractive method for ion structural characterization and isomer differentiation. The energetics, thermochemistry and dynamics of surface-induced charge inversion of nitrobenzene and other substituted aromatics is discussed. Reactive collisions also occur between gaseous ions and surfaces and the reactions depend on the chemical nature of the collision partners. These reactions can be used for selected chemical modifications of surfaces as well as for surface analysis. Particular emphasis is given here to one ion/surface interaction, ion soft-landing, a process in which the projectile ion is landed intact at the surface, either as the corresponding neutral molecule or, interestingly but less commonly, in the form of the ion itself. The ion soft-landing experiment allows preparative mass spectrometry, for example the preparation of pure biological compounds by using the mass spectrometer as a separation device. After separation, the mass-selected ions are collected by soft-landing, at different spatial points in an array. If the experiment is done using a suitable liquid medium, at least some proteins retain their biological activity.
2005. "Model Identity Sn2 Reactions CH₃X + X- (X = F, Cl, CN, OH, SH, NH₂, PH₂): Marcus Theory Analyzed." Journal of Physical Chemistry A 109(46):10613-10628. Abstract Abstract not currently available for review at this time.
2005. "Thermodynamic Properties of Molecular Borane Phosphines, Alane Amines, and Phosphine Alanes and the [BH4-][PH4+], [AIH4-][NH4+], and [AIH4-][PH4+] Salts for Chemical Hydrogen Storage Systems from ab Initio Electronic Structure Theory." Journal of Physical Chemistry A 109(44):10138-10147. doi:10.1021/jp054152y Abstract An abstract for this journal article is not available at this time.
2005. "Progressive Thermal Desorption of Vapor Mixtures from a Preconcentrator with a Porous Metal Foam Internal Architecture and Variable Thermal Ramp Rates." Analytical Chemistry 77(6):1867-1875. doi:10.1021/ac049142s Abstract A vapor preconcentrator has been designed with the porous polymer (Tenax) packed into a highly porous metal foam to facilitate thermal conductivity and temperature uniformity throughout the bed of the preconcentrator during heating. Vapors were desorbed using linear temperature programming from room temperature to a maximum temperature of 170ºC or 200ºC; the programmed duration of the thermal ramp was varied from 10 to 180 seconds. The thermal desorption of vapor mixtures captured on the preconcentrator has been examined in detail, using methyl ethyl ketone, toluene, and dimethyl methylphosphonate as a test mixture. Vapors desorbed as a sequence of partially separated overlapping peaks as observed with a polymer-coated flexural plate wave sensor. It was shown that vapor mixture resolution improved as the total time of the thermal ramp was extended from 30 seconds to 120 seconds. In this way the preconcentrator serves to act as a preseparator in addition to its usual functions for sampling, signal modulation, and improving sensitivity. Overlapping peaks were modeled and peak areas were extracted using an exponentially modified Gaussian model. Peak areas were independent of the thermal ramp rate. Uses of such preconcentrators with multivariate detectors such as sensor arrays are discussed.
2005. "Cobalt-Doped Anatase TiO2: A Room Temperature Dilute Magnetic Dielectric Material." Journal of Applied Physics 97:10D320. Abstract Structural and magnetic properties of epitaxial CoxTi₁-xO₂ films with x~2%, grown by RF magnetron sputtering from composite oxide targets on lattice matched LaAIO₃(001) substrates have been investigated. The films were sputtered at a deposition rate of ~0.12 Å/s for a range of substrate temperatures from 300°C to 750°C, followed by UHV annealing for 1 hr at 400°C and aging in air for 3 months. XRD experiments determine the best quality of highly oriented anatase (991) phase in films deposited 500-750°C. Magnetic hysteresis loops at 5K and 300K and thermoremanence measurements from 5-365 K show ferromagnetism in all samples in the whole temperature range. Annealing and aging lead to an increase of spontaneous moment an order of magnitude of up to ~1.1 µB/ Co atom at 300 K. As=deposited, annealed, and aged films were found to be highly resistive changes both in surface morphology and distribution of spontaneous magnetization in the annealed films. Possible mechanisms of the ferromagnetic behavior of such dielectric transition metal-doped oxides will be discussed.
2005. "Intrinsic Ferromagnetism in Insulating Cobalt Doped Anatase TiO₂ ." Physical Review Letters 94(15):Art. No. 157204. Abstract Using complementary experiments we show that the room temperature ferromagnetism observed in anatase Co:TiO₂ films is not carrier mediated, but coexists with the dielectric state. TEM and x-ray absorption spectroscopy reveal a solid solution of Co in anatase, where Co is not metallic but in the +2 state substituting for Ti. Measurements at 300 K yield a Ms of 1.1 µB/Co atom, while all films are highly insulating. The evidence of intrinsic ferromagnetism in the dielectric ground state of Co:TiO₂ leads to new considerations for the origin of ferromagnetism in transition metal doped oxides.
2005. "Aluminum Nitride-Silicon Carbide Alloy Crystals Grown on SiC Substrates by Sublimation." MRS Internet Journal of Nitride Semiconductor Research 10(5):1-8. Abstract AlN-SiC alloy crystals, with a thickness greater than 500 µm, were grown on 4H- and 6H-SiC substrates from a mixture of AlN and SiC powders by the sublimation-recondensation method at 1860-1990 °C. On-axis SiC substrates produced a rough surface covered with hexagonal grains, while 6H- and 4H- off-axis SiC substrates with different miscut angles (8° or 3.68°) formed a relatively smooth surface with terraces and steps. The substrate misorientation ensured that the AlN-SiC alloy crystals grew two dimensionally as identified by scanning electron microscopy (SEM). X-ray diffraction (XRD) and transmission electron microscopy (TEM) confirmed that the AlN-SiC alloys had the wurtzite structure. Electron probe microanalysis (EPMA) and x-ray photoelectron spectroscopy (XPS) demonstrated that the resultant alloy crystals had non-stoichiometric ratios of Al:N and Si:C and a uniform composition throughout the alloy crystal from the interface to the surface. The composition ratio of Al:Si of the alloy crystals changed with the growth temperature, and differed from the original source composition, which was consistent with the results predicted by thermodynamic calculation of the solid-vapor distribution of each element. XPS detected the bonding between Si-C, Si-N, Si-O for the Si 2p spectra. The dislocation density decreased with the growth, which was lower than 106 cm-2 at the alloy surface, more than two orders of magnitude lower compared to regions close to the crystal/substrate interface, as determined by TEM.
2005. "Nano-Scaffold Mediates Hydrogen Release and Reactivity of Ammonia Borane." Angewandte Chemie International Edition 44(23):3578-3582. Abstract One of the imposing barriers to realizing the promise of an energy economy based on hydrogen is onboard hydrogen storage for fuel-cell-powered vehicles. New materials that enable the release of dense, plentiful and pure hydrogen at temperatures less than 85 ºC are necessary to move the world from an oil-based economy to a hydrogen economy. We report a novel approach in which we deposit a hydrogen-rich material into a nanoporous scaffold. The role of the scaffold is to impose a nano-phase structure on the hydrogen-rich material thus providing an additional handle on the kinetics and thermodynamics of hydrogen release. We demonstrate on the example of ammonia borane infused in the nanoporous silica that the kinetics of hydrogen release is improved while the purity of hydrogen is increased in comparison with the release from bulk ammonia borane. These findings suggest that hydrogen rich materials infused in nanoscaffolds offer the most promising approach to date for onboard hydrogen storage